We did a driving tour of New England early last October. Flew to NY, spent a few days there and then drove to Cape Cod, Boston and onwards for some leaf peeking!
Make sure you head to Provincetown for a day/night, fab place! As Cape Cod is small enough i would stay someplace for a few days and then do day tours from there. Nantucket and Martha's vineyard are lovely spots as well. We stayed in Hyannis for a couple of nights but to be honest i would not ruch back there - good for a bit of shopping but gone a bit run down in my view. I would stay someplace mid cape and then explore the area from there. Maybe a holiday home to rent?
We stayed in the Hilton Financial District in Boston - very well located.
Fab part of the world - am v. jealous!!